Dear People,
This may not be the right place to ask a question about Rmpi, but I don't
know of a better one.
I am trying to get a simple program working using Rmpi with the model of 1
R master and n C slaves. What I am trying to do is have each of the C
slaves generate a random number from U[0,1], and then have the master
collect all n numbers as a vector and output it. However even doing this
is rather over my head. I'm trying to use rsprng and sprng, but I am sure
what I am currently doing is wrong.
I enclose a first attempt. Any suggestions would be appreciated. Thanks in
advance.
Faheem.
*************************************************************************
rand.R
*************************************************************************
library(Rmpi)
rand <- function ()
{
if (mpi.comm.size(1) > 1)
stop ("It seems some slaves running on comm 1.")
mpi.comm.spawn("./rand")
mpi.intercomm.merge(2,0,1)
mpi.init.sprng()
free.sprng() #does this function exist here?
rdata <- double(sum(mpi.comm.size(1)))
out <- mpi.gather(0, 2, rdata) ##this isn't right
mpi.comm.free()
out
}
*************************************************************************
rand.c
*************************************************************************
#include <mpi.h>
#include <sprng.h>
int main(int argc, char **argv)
{
double rand;
double* randarray;
MPI_Comm slavecomm, all_processes;
/*Initialize MPI*/
MPI_Init(&argc, &argv);
MPI_Comm_get_parent(&slavecomm);
MPI_Intercomm_merge(slavecomm, 1, &all_processes);
/*How many processes are there?*/
MPI_Comm_size(all_processes, &size);
/*Which one am I?*/
MPI_Comm_rank(all_processes, &rank);
init_sprng()
rand = sprng();
free.sprng()
randarray = (double *)malloc(sizeof(double)*size);
/*Gather random numbers from all C slave processes*/
/* Using randarray doesn't make sense since this should correspond
to the rdata vector in the R master process */
MPI_GAther(&rand, 1, 1, MPI_DOUBLE, randarray, 1, MPI_DOUBLE, 0,
all_processes);
/*All done*/
MPI_Comm_free(&all_processes);
MPI_Finalize();
exit(0);
}
use snow. The general approach highlighted in http://www.analytics.washington.edu/~rossini/courses/cph-statcomp in Lab 4 works with Rmpi as well. Faheem Mitha <faheem at email.unc.edu> writes:> Dear People, > > This may not be the right place to ask a question about Rmpi, but I don't > know of a better one. > > I am trying to get a simple program working using Rmpi with the model of 1 > R master and n C slaves. What I am trying to do is have each of the C > slaves generate a random number from U[0,1], and then have the master > collect all n numbers as a vector and output it. However even doing this > is rather over my head. I'm trying to use rsprng and sprng, but I am sure > what I am currently doing is wrong. > > I enclose a first attempt. Any suggestions would be appreciated. Thanks in > advance. > > Faheem. > > ************************************************************************* > rand.R > ************************************************************************* > library(Rmpi) > > rand <- function () > { > if (mpi.comm.size(1) > 1) > stop ("It seems some slaves running on comm 1.") > mpi.comm.spawn("./rand") > mpi.intercomm.merge(2,0,1) > > mpi.init.sprng() > free.sprng() #does this function exist here? > > rdata <- double(sum(mpi.comm.size(1))) > out <- mpi.gather(0, 2, rdata) ##this isn't right > mpi.comm.free() > out > } > > ************************************************************************* > rand.c > ************************************************************************* > #include <mpi.h> > #include <sprng.h> > > int main(int argc, char **argv) > { > double rand; > double* randarray; > > MPI_Comm slavecomm, all_processes; > > /*Initialize MPI*/ > MPI_Init(&argc, &argv); > > MPI_Comm_get_parent(&slavecomm); > MPI_Intercomm_merge(slavecomm, 1, &all_processes); > > /*How many processes are there?*/ > MPI_Comm_size(all_processes, &size); > > /*Which one am I?*/ > MPI_Comm_rank(all_processes, &rank); > > init_sprng() > rand = sprng(); > free.sprng() > > randarray = (double *)malloc(sizeof(double)*size); > > /*Gather random numbers from all C slave processes*/ > /* Using randarray doesn't make sense since this should correspond > to the rdata vector in the R master process */ > MPI_GAther(&rand, 1, 1, MPI_DOUBLE, randarray, 1, MPI_DOUBLE, 0, all_processes); > > /*All done*/ > MPI_Comm_free(&all_processes); > MPI_Finalize(); > exit(0); > } > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help >-- rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
On 1 Dec 2003, Faheem Mitha spake thusly:> I am trying to get a simple program working using Rmpi with the model of 1 > R master and n C slaves. What I am trying to do is have each of the C > slaves generate a random number from U[0,1], and then have the master > collect all n numbers as a vector and output it. However even doing this > is rather over my head. I'm trying to use rsprng and sprng, but I am sure > what I am currently doing is wrong. > > ************************************************************************* > rand.R > ************************************************************************* > library(Rmpi) > > rand <- function () > { > if (mpi.comm.size(1) > 1) > stop ("It seems some slaves running on comm 1.") > mpi.comm.spawn("./rand") > mpi.intercomm.merge(2,0,1) > >X mpi.init.sprng() >X free.sprng() #does this function exist here?I'm not familiar with Rmpi code. But here you don't need call any SPRNG function. Instead, generate a seed (an integer) can pass it on to the slaves.> rdata <- double(sum(mpi.comm.size(1))) > out <- mpi.gather(0, 2, rdata) ##this isn't right > mpi.comm.free() > out > } > > ************************************************************************* > rand.c > ************************************************************************* > #include <mpi.h> > #include <sprng.h> > > int main(int argc, char **argv) > { > double rand; > double* randarray; > > MPI_Comm slavecomm, all_processes; > > /*Initialize MPI*/ > MPI_Init(&argc, &argv); > > MPI_Comm_get_parent(&slavecomm); > MPI_Intercomm_merge(slavecomm, 1, &all_processes); > > /*How many processes are there?*/ > MPI_Comm_size(all_processes, &size); > > /*Which one am I?*/ > MPI_Comm_rank(all_processes, &rank); > >X init_sprng() >X rand = sprng(); >X free.sprng()Receive the seed from the master and call int * stream_id; stream_id = init_sprng (gtype, rank, size, seed, param); where gtype and param can be predefined or got from the master as well. Now you can generate random numbers by: rand = sprng (stream_id); free_sprng (stream_id);> randarray = (double *)malloc(sizeof(double)*size); > > /*Gather random numbers from all C slave processes*/ > /* Using randarray doesn't make sense since this should correspond > to the rdata vector in the R master process */ > MPI_GAther(&rand, 1, 1, MPI_DOUBLE, randarray, 1, MPI_DOUBLE, 0, > all_processes); > > /*All done*/ > MPI_Comm_free(&all_processes); > MPI_Finalize(); > exit(0); > }There is nothing mysterious about the MPI code in SPRNG, don't use it. Generating and passing seeds around yourself. Michael -- Na (Michael) Li, Ph.D. Assistant Professor Division of Biostatistics, University of Minnesota A443 Mayo Bldg, MMC 303 Phone: (612) 626-4765 420 Delaware St SE Fax: (612) 626-0660